Design and construction of synthetic gene networks in mammalian cells

Methods in Molecular Biology

Volumn 813, Issue , 2012, Pages 359-376

  Karlsson, Maria ^a,b   Weber, Wilfried ^a,b   Fussenegger, Martin ^c  

^a UNIVERSITY OF FREIBURG   (Germany)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Auxin; Boolean logic; Degron; Inducible expression; NOR gate

Indexed keywords

F BOX PROTEIN; INDOLEACETIC ACID DERIVATIVE; MYC PROTEIN; TETRACYCLINE;

ARTICLE; CELL STRAIN HEK293; CULTURE TECHNIQUE; DRUG EFFECT; GENE REGULATORY NETWORK; GENETIC TRANSFECTION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROMOTER REGION; REPORTER GENE; REPRODUCIBILITY; SYNTHETIC BIOLOGY; TRANSCRIPTION INITIATION; WESTERN BLOTTING;

BLOTTING, WESTERN; CELL CULTURE TECHNIQUES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; F-BOX PROTEINS; GENE REGULATORY NETWORKS; GENES, REPORTER; HEK293 CELLS; HUMANS; INDOLEACETIC ACIDS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEINS C-MYC; REPRODUCIBILITY OF RESULTS; SYNTHETIC BIOLOGY; TETRACYCLINE; TRANSCRIPTIONAL ACTIVATION; TRANSFECTION;

EID: 82355171209     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-412-4_22     Document Type: Article

References (37)

1. Weber, W., and Fussenegger, M. (2010) Synthetic gene networks in mammalian cells, Curr Opin Biotechnol 692, 235-249.
2. Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells, Nat Biotechnol 25, 795-801. (Pubitemid 47052185)
3. Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells, Biotechnol Bioeng 87, 478-484. (Pubitemid 39150049)
4. Deans, T. L., Cantor, C. R., and Collins, J. J. (2007) A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells, Cell 130, 363-372. (Pubitemid 47081136)
5. Kramer, B. P., and Fussenegger, M. (2005) Hysteresis in a synthetic mammalian gene network, Proc Natl Acad Sci USA 102, 9517-9522. (Pubitemid 40981713)
6. Kramer, B. P., Viretta, A. U., Daoud-El-Baba, M., Aubel, D., Weber, W., and Fussenegger, M. (2004) An engineered epigenetic transgene switch in mammalian cells, Nat Biotechnol 22, 867-870. (Pubitemid 38886606)
7. Weber, W., Stelling, J., Rimann, M., Keller, B., Daoud-El Baba, M., Weber, C. C., Aubel, D., and Fussenegger, M. (2007) A synthetic timedelay circuit in mammalian cells and mice, Proc Natl Acad Sci USA 104, 2643-2648. (Pubitemid 46327933)
8. Tigges, M., Marquez-Lago, T. T., Stelling, J., and Fussenegger, M. (2009) A tunable synthetic mammalian oscillator, Nature 457, 309-312.
9. Swinburne, I. A., Miguez, D. G., Landgraf, D., and Silver, P. A. (2008) Intron length increases oscillatory periods of gene expression in animal cells, Genes Dev 22, 2342-2346.
10. Weber, W., and Fussenegger, M. (2006) Pharmacologic transgene control systems for gene therapy, J Gene Med 8, 535-556. (Pubitemid 43827248)
11. Malphettes, L., and Fussenegger, M. (2004) Macrolide- and tetracycline-adjustable siRNAmediated gene silencing in mammalian cells using polymerase II-dependent promoter derivatives, Biotechnol Bioeng 88, 417-425. (Pubitemid 39536544)
12. Greber, D., El-Baba, M. D., and Fussenegger, M. (2008) Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch, Nucleic Acids Res 36, e101.
13. Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T., and Kanemaki, M. (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells, Nat Methods 6, 917-922.
14. Banaszynski, L. A., Chen, L. C., Maynard-Smith, L. A., Ooi, A. G., and Wandless, T. J. (2006) A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules., Cell 126, 995-1004. (Pubitemid 44310772)
15. Mitta, B., Rimann, M., Ehrengruber, M. U., Ehrbar, M., Djonov, V., Kelm, J., and Fussenegger, M. (2002) Advanced modular self-inactivating lentiviral expression vectors for multigene interventions in mammalian cells and in vivo transduction, Nucleic Acids Res 30, e113.
16. Fussenegger, M., Morris, R. P., Fux, C., Rimann, M., von Stockar, B., Thompson, C. J., and Bailey, J. E. (2000) Streptogramin-based gene regulation systems for mammalian cells, Nat Biotechnol 18, 1203-1208.
17. Sambrook, J., Fritsch, E. F., and Maniatis, T. (2000) Molecular Cloning, A Laboratory Manual, 3rd ed, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
18. Fritze, C. E., and Anderson, T. R. (2000) Epitope tagging: general method for tracking recombinant proteins, Methods Enzymol 327, 3-16. (Pubitemid 34193294)
19. Kain, S. R., and Ganguly, S. (2001) Overview of genetic reporter systems, Curr Protoc Mol Biol 9, 9.6.
20. Schlatter, S., Rimann, M., Kelm, J., and Fussenegger, M. (2002) SAMY, a novel mammalian reporter gene derived from Bacillus stearothermophilus alpha-amylase, Gene 282, 19-31. (Pubitemid 34117558)
21. Weber, W., Rimann, M., Spielmann, M., Keller, B., Daoud-El Baba, M., Aubel, D., Weber, C. C., and Fussenegger, M. (2004) Gas-inducible transgene expression in mammalian cells and mice, Nat Biotechnol 22, 1440-1444. (Pubitemid 39482865)
22. Hartenbach, S., Daoud-El Baba, M., Weber, W., and Fussenegger, M. (2007) An engineered L-arginine sensor of Chlamydia pneumoniae enables arginine-adjustable transcription control in mammalian cells and mice, Nucleic Acids Res 35, e136.
23. Weber, W., Lienhart, C., Daoud El-Baba, M., and Fussenegger, M. (2009) A biotin-triggered genetic switch in mammalian cells and mice, Metab Eng 11, 117-124.
24. Mullick, A., Xu, Y., Warren, R., Koutroumanis, M., Guilbault, C., Broussau, S., Malenfant, F., Bourget, L., Lamoureux, L., Lo, R., Caron, A. W., Pilotte, A., and Massie, B. (2006) The cumate gene-switch: a system for regulated expression in mammalian cells, BMC Biotechnol 6, 43.
25. Weber, W., Marty, R. R., Link, N., Ehrbar, M., Keller, B., Weber, C. C., Zisch, A. H., Heinzen, C., Djonov, V., and Fussenegger, M. (2003) Conditional human VEGF-mediated vascularization in chicken embryos using a novel temperature-inducible gene regulation (TIGR) system, Nucleic Acids Res 31, e69.
26. Weber, W., Fux, C., Daoud-el Baba, M., Keller, B., Weber, C. C., Kramer, B. P., Heinzen, C., Aubel, D., Bailey, J. E., and Fussenegger, M. (2002) Macrolide-based transgene control in mammalian cells and mice, Nat Biotechnol 20, 901-907. (Pubitemid 35001127)
27. Malphettes, L., Weber, C. C., El-Baba, M. D., Schoenmakers, R. G., Aubel, D., Weber, W., and Fussenegger, M. (2005) A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1, Nucleic Acids Res 33, e107.
28. Weber, W., Link, N., and Fussenegger, M. (2006) A genetic redox sensor for mammalian cells, Metab Eng 8, 273-280.
29. Weber, W., Schoenmakers, R., Spielmann, M., El-Baba, M. D., Folcher, M., Keller, B., Weber, C. C., Link, N., van de Wetering, P., Heinzen, C., Jolivet, B., Sequin, U., Aubel, D., Thompson, C. J., and Fussenegger, M. (2003) Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice, Nucleic Acids Res 31, e71.
30. Gossen, M., and Bujard, H. (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters, Proc Natl Acad Sci USA 89, 5547-5551.
31. Gossen, M., Freundlieb, S., Bender, G., Muller, G., Hillen, W., and Bujard, H. (1995) Transcriptional activation by tetracyclines in mammalian cells, Science 268, 1766-1769.
32. Neddermann, P., Gargioli, C., Muraglia, E., Sambucini, S., Bonelli, F., De Francesco, R., and Cortese, R. (2003) A novel, inducible, eukaryotic gene expression system based on the quorum-sensing transcription factor TraR, EMBO Rep 4, 159-165. (Pubitemid 36322157)
33. Gitzinger, M., Kemmer, C., Daoud-El Baba, M., Weber, W., and Fussenegger, M. (2009) Controlling transgene expression in subcutaneous implants using a skin lotion containing the apple metabolite phloretin, Proc Natl Acad Sci USA 106, 10638-10643.
34. Malphettes, L., Schoenmakers, R. G., and Fussenegger, M. (2006) 6-hydroxy-nicotineinducible multilevel transgene control in mammalian cells, Metab Eng 8, 543-553. (Pubitemid 44512164)
35. Weber, W., Malphettes, L., de Jesus, M., Schoenmakers, R., El-Baba, M. D., Spielmann, M., Keller, B., Weber, C. C., van de Wetering, P., Aubel, D., Wurm, F. M., and Fussenegger, M. (2005) Engineered Streptomyces quorumsensing components enable inducible siRNAmediated translation control in mammalian cells and adjustable transcription control in mice, J Gene Med 7, 518-525. (Pubitemid 40553132)
36. Yao, F., Svensjo, T., Winkler, T., Lu, M., Eriksson, C., and Eriksson, E. (1998) Tetracycline repressor, tetR, rather than the tetR-mammalian cell transcription factor fusion derivatives, regulates inducible gene expression in mammalian cells, Hum Gene Ther 9, 1939-1950. (Pubitemid 28439099)
37. Kemmer, C., Gitzinger, M., Daoud-El Baba, M., Djonov, V., Stelling, J., and Fussenegger, M. (2010) Self-sufficient control of urate homeostasis in mice by a synthetic circuit, Nat Biotechnol 28, 355-360.